Programming In the Life Sciences
This is an OER around a six day course on using JavaScript to program the life sciences web, with a focus on the life sciences content in Wikidata and its API.
Description of the course
In the life sciences the physical interactions between chemical and biological entities, like genes, RNA, proteins, metabolites, and drugs, is of key interest. Not only do these interactions play an important role in the regulation of gene expression, inhibition of proteins, and they basically define all cellular processes and therefore life itself. For example, pharmacology studies the action of drugs on protein, metabolism depends on the interactions of small molecule substrates with enzymes, and coronaviruses reorganize the normal function of cells after entry into the cell.
With the increasing amount of knowledge and data in the life sciences, automation becomes increasingly important. The data, whether large or small and complex, have challenges to integrate data from different experiments and data sources. Many core life sciences databases provide SPARQL end points to their knowledge, while Wikidata is a spider in this web of semantic data. In this course, you will learn to use how to interact with SPARQL endpoints with JavaScript and visualize the results graphically with a library like d3.js or Cytoscape.js.
Objectives
- To have the ability to recognize various classes of chemical entities in biology and to understand the basic physical and chemical interactions between them.
- To know the programming concepts related to data processing and web services.
- To be familiar with technologies for web services and querying resources in the life sciences.
- To obtain experience in using such web services with a programming language.
- To be able to select web services for a particular biological research question.
- To be familiar with modern software development practices.
- To have the ability to visualize data retrieved from webservices
Literature
- “JavaScript & jQuery: The Missing Manual” by D.S. McFarland (O’Reilly, 2nd edition, 2011)
- “Wikidata as a knowledge graph for the life sciences” by A. Waagmeester et al. eLife, 2020, https://doi.org/10.7554/eLife.52614
- “WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research” by D. Slenter et al. NAR, 2018, https://doi.org/10.1093/NAR/GKX1064
- “Semantic Web programming” by J. Hebeler. 2009. UB Library
- “Semantic Web for the working ontologist: effective modeling in RDFS and OWL” by D. Allemang, J.A. Hendler. 2011. UB Library
- “Git from the Bottom Up” by J. Wiegley. https://jwiegley.github.io/git-from-the-bottom-up/